The IPD-IMGT/HLA Database - New developments in reporting HLA variation.

IPD-IMGT/HLA is a constituent of the Immuno Polymorphism Database (IPD), which was developed to provide a centralised system for the study of polymorphism in genes of the immune system. The IPD project works with specialist groups of nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The primary database within the IPD project is the IPD-IMGT/HLA Database, which provides a locus-specific database for the hyper-polymorphic allele sequences of the genes in the HLA system, also known as the human Major Histocompatibility Complex. The IPD-IMGT/HLA Database was first released over 17 years ago, building on the work of the WHO Nomenclature Committee for Factors of the HLA system that was initiated in 1968. The IPD-IMGT/HLA Database enhanced this work by providing the HLA community with an online, searchable repository of highly curated HLA sequences. Many of the genes encode proteins of the immune system and are hyper polymorphic, with some genes currently having over 4000 known allelic variants. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website, http://www.ebi.ac.uk/ipd/imgt/hla.

[1]  James Robinson,et al.  The IMGT/HLA database , 2008, Nucleic Acids Res..

[2]  Sue Povey,et al.  Gene map of the extended human MHC , 2004, Nature Reviews Genetics.

[3]  R. Wilson,et al.  Modernizing Reference Genome Assemblies , 2011, PLoS biology.

[4]  Johan T den Dunnen,et al.  Describing structural changes by extending HGVS sequence variation nomenclature , 2011, Human mutation.

[5]  M. Callaham,et al.  Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem. , 2013, FEMS microbiology ecology.

[6]  Harriet Noreen,et al.  Common and well-documented HLA alleles: report of the Ad-Hoc committee of the american society for histocompatiblity and immunogenetics. , 2007, Human immunology.

[7]  Effie W Petersdorf,et al.  Effect of T-cell-epitope matching at HLA-DPB1 in recipients of unrelated-donor haemopoietic-cell transplantation: a retrospective study. , 2012, The Lancet. Oncology.

[8]  Miss A.O. Penney (b) , 1974, The New Yale Book of Quotations.

[9]  Guy Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[10]  Barbara Bruno,et al.  Nonpermissive HLA-DPB1 disparity is a significant independent risk factor for mortality after unrelated hematopoietic stem cell transplantation. , 2009, Blood.

[11]  Takashi Gojobori,et al.  The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments , 2011, Nucleic Acids Res..

[12]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[13]  Katharina Fleischhauer,et al.  Frequency and targeted detection of HLA-DPB1 T cell epitope disparities relevant in unrelated hematopoietic stem cell transplantation. , 2007, Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation.

[14]  I. Dunham,et al.  DNA sequence and analysis of human chromosome 9 , 2003, Nature.

[15]  Rodrigo Lopez,et al.  Web Services at the European Bioinformatics Institute , 2007, Nucleic Acids Res..

[16]  Martin Maiers,et al.  The impact of amino acid variability on alloreactivity defines a functional distance predictive of permissive HLA-DPB1 mismatches in hematopoietic stem cell transplantation. , 2015, Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation.

[17]  W. Klitz,et al.  Common and well-documented HLA alleles: 2012 update to the CWD catalogue. , 2013, Tissue antigens.

[18]  G. Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[19]  J G Bodmer,et al.  HLA class II nucleotide sequences, 1992. , 1993, Immunogenetics.

[20]  J G Bodmer,et al.  HLA CLASS II NUCLEOTIDE SEQUENCES, 1991 , 1991, Human immunology.

[21]  S. Krishnakumar,et al.  High-throughput, high-fidelity HLA genotyping with deep sequencing , 2012, Proceedings of the National Academy of Sciences.

[22]  S. Antonarakis,et al.  Corrigendum: Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion , 2002, Human mutation.

[23]  J G Bodmer,et al.  Sequencing-based typing reveals new insight in HLA-DPA1 polymorphism. , 1994, Tissue antigens.

[24]  Terasaki Pi,et al.  Nomenclature for factors of the HL-a system. , 1998, Bulletin of the World Health Organization.

[25]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[26]  W R Mayr,et al.  Nomenclature for factors of the HLA system, 1991. , 1992, Vox sanguinis.

[27]  Julia G. Bodmer,et al.  HLA-DRB nucleotide sequences, 1990 , 2004, Immunogenetics.

[28]  S. Ranade,et al.  HLA Typing for the Next Generation , 2015, PloS one.

[29]  I. Dunham,et al.  The DNA sequence and analysis of human chromosome 6 , 2003, Nature.

[30]  Maria Pia Sormani,et al.  A T-cell epitope encoded by a subset of HLA-DPB1 alleles determines nonpermissive mismatches for hematologic stem cell transplantation. , 2003, Blood.

[31]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[32]  James Robinson,et al.  The IPD and IMGT/HLA database: allele variant databases , 2014, Nucleic Acids Res..

[33]  Matthew W. Anderson,et al.  A multi-site study using high-resolution HLA genotyping by next generation sequencing. , 2011, Tissue antigens.

[34]  M. Boyce-Jacino,et al.  HLA class I sequence-based typing. , 1993, Human immunology.

[35]  James G. R. Gilbert,et al.  The vertebrate genome annotation (Vega) database , 2004, Nucleic Acids Res..

[36]  S Mackinnon,et al.  Diverging effects of HLA–DPB1 matching status on outcome following unrelated donor transplantation depending on disease stage and the degree of matching for other HLA alleles , 2010, Leukemia.

[37]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[38]  Gautier Koscielny,et al.  Ensembl 2012 , 2011, Nucleic Acids Res..

[39]  C Anasetti,et al.  Role of the mixed lymphocyte culture reaction in predicting acute graft-versus-host disease after marrow transplants from haploidentical and unrelated donors. , 1993, Transplantation proceedings.

[40]  W R Mayr,et al.  Nomenclature for factors of the HLA system, 1991. , 1992, Human immunology.

[41]  P Parham,et al.  HLA class I nucleotide sequences, 1991. , 1991, Human immunology.

[42]  Ying Cheng,et al.  Major submissions tool developments at the European nucleotide archive , 2011, Nucleic Acids Res..

[43]  Rodrigo Lopez,et al.  A new bioinformatics analysis tools framework at EMBL–EBI , 2010, Nucleic Acids Res..